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Analysis extensions #812

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Analysis extensions #812

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bcorrie
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@bcorrie bcorrie commented May 20, 2024

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bcorrie and others added 30 commits May 14, 2024 21:31
@bcorrie
Fix HTML error
8026fa9
@bcorrie
Revert change to directory. Don't want Apps to have to know about
2a3bdff 
Tapis.
@bcorrie
Finished an intitial app for testing.
89bd09c
@bcorrie
Add a hint for downloads - yes or no
6994950
@bcorrie
Reorder the apps so there is some structure to the list
064ada8
@StyleCIBot
Apply fixes from StyleCI
d1e3d0b
@bcorrie
Merge pull request #809 from sfu-ireceptor/analysis-O37rbR
9b657cf 
Apply fixes from StyleCI
@bcorrie
Fix fields file.
c50a588
@bcorrie
Fixes for CA cert bundle, add JSON to TSV
94873e6
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
eda39e5 
…r/gateway into analysis-extensions
@bcorrie
Minor doc and name fixes
b01dba2
@bcorrie
Add HTML table
483d9ff
@bcorrie
Change the default CDR motif
89b74cf
@bcorrie
Added style directives to HTML to get a decent table
4d5fc1f
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
0483abe 
…r/gateway into analysis-extensions
@bcorrie
Added code to track an App's requirements for data download.
f984bad
@bcorrie
Initial functionality to skip downloads.
207c81a 
Working but manifest is not being generated correctly.
@StyleCIBot
Apply fixes from StyleCI
3e08438
@bcorrie
Merge pull request #810 from sfu-ireceptor/analysis-kYbR9A
8f5c111 
Apply fixes from StyleCI
@bcorrie
Fix bugs for case when data is not downloaded.
5aec742
@bcorrie
Use the short job queue for jobs that don't download data.
6fe7258
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
5d3e502 
…r/gateway into analysis-extensions
@StyleCIBot
Apply fixes from StyleCI
f96b573
@bcorrie
Merge pull request #811 from sfu-ireceptor/analysis-e0bjJ2
236341a 
Apply fixes from StyleCI
@bcorrie
Added Cell ability to handle no downloads
4b3683a
@bcorrie
Added no download capabilities.
6c1cce7
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
c31d527 
…r/gateway into analysis-extensions
@StyleCIBot
Apply fixes from StyleCI
3334aa1
@bcorrie
Merge pull request #813 from sfu-ireceptor/analysis-Q3ZEGw
33b837b 
Apply fixes from StyleCI
@bcorrie
Fix bug in info file generation.
e7c74a3
bcorrie and others added 27 commits May 20, 2024 20:05
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
43def68 
…r/gateway into analysis-extensions
@bcorrie
Cleaned up listing of Apps
7f090ed
@bcorrie
Removed test parameter
e573e36
@bcorrie
Fix exception handling bug
bc850dc
@bcorrie
Split URLs so on separate lines, add new fields.
5cff059
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
315be40 
…r/gateway into analysis-extensions
@bcorrie
Minor changes to names/docs.
896224c
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
d82ca2c 
…r/gateway into analysis-extensions
@StyleCIBot
Apply fixes from StyleCI
05bf2ef
@bcorrie
Merge pull request #814 from sfu-ireceptor/analysis-dj6AYg
7f290cc 
Apply fixes from StyleCI
@bcorrie
Add cell_id to field that can be searched for cell and rearrangement
977739b
@bcorrie
Restructure ir_hints in config file.
1f55879 
Now can have both requirements needed for an App to work and resources
(cpu, memory) that are required by the App to complete.
@StyleCIBot
Apply fixes from StyleCI
f3678dc
@bcorrie
Merge pull request #815 from sfu-ireceptor/analysis-APMowG
4e82b4c 
Apply fixes from StyleCI
@bcorrie
Restructure directory names for consistency
2c15197
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
fcb222d 
…r/gateway into analysis-extensions
@bcorrie
Change immunarch directory name.
90ff432
@bcorrie
Clean up tabs, add message if over resource usage.
05440c8
@bcorrie
Add ability to generate message if resource usage is over the limit.
0267541
@StyleCIBot
Apply fixes from StyleCI
eb90dd6
@bcorrie
Merge pull request #816 from sfu-ireceptor/analysis-7Wdkpk
a2ee7fb 
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@bcorrie
Add timing info to base app.
6e89111
@bcorrie
Add check on run time if app has a run time hint.
d635be5
@StyleCIBot
Apply fixes from StyleCI
ba3eb9c
@bcorrie
Merge pull request #817 from sfu-ireceptor/analysis-16Bdgy
96c0b25 
Apply fixes from StyleCI
@bcorrie
Update apps to have appropriate resource limits.
77aa65e 
In most cases these are empty, as we don't have limits for any
Apps excepty Immunarch.
@bcorrie
Merge branch 'analysis-extensions' of https://github.com/sfu-irecepto…
ce0a2f9 
…r/gateway into analysis-extensions
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@bcorrie @StyleCIBot